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comparison tandem.xml @ 14:9d6e0ad4d600 draft

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Docker support and update for protk 1.4
author iracooke
date Thu, 26 Mar 2015 19:53:53 -0400
parents c60d1f18fd85
children 0faaab4f192a
comparison
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13:c60d1f18fd85 14:9d6e0ad4d600
1 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.2"> 1 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.0">
2 2
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3.0">protk</requirement> 4 <container type="docker">iracooke/protk-1.4.1</container>
5 <requirement type="package" version="1.4">protk</requirement>
5 </requirements> 6 </requirements>
6 7
7 <description>Run an X!Tandem Search</description> 8 <description>Run an X!Tandem Search</description>
8 9
9 <command> 10 <command>
42 43
43 -v $missed_cleavages 44 -v $missed_cleavages
44 45
45 -f $fragment_ion_tol 46 -f $fragment_ion_tol
46 47
47 -p $precursor_ion_tol 48 -p $precursor_ion_tol
48 49
49 $allow_multi_isotope_search 50 $allow_multi_isotope_search
50 51
51 $acetyl_protein_nterm 52 $acetyl_protein_nterm
52 53
84 <option value="input_ref">Custom parameter file</option> 85 <option value="input_ref">Custom parameter file</option>
85 </param> 86 </param>
86 <when value="built_in"> 87 <when value="built_in">
87 <param name="paramskey" type="select" format="text" > 88 <param name="paramskey" type="select" format="text" >
88 <label>Paramset</label> 89 <label>Paramset</label>
90 <option value="isb_kscore">ISB K-Score (Recommended for TPP)</option>
91 <option value="isb_native">ISB Native</option>
89 <option value="gpm">GPM</option> 92 <option value="gpm">GPM</option>
90 <option value="isb_native">ISB Native</option>
91 <option value="isb_kscore">ISB K-Score</option>
92 </param> 93 </param>
93 </when> 94 </when>
94 <when value="input_ref"> 95 <when value="input_ref">
95 <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" /> 96 <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />
96 </when> 97 </when>
130 131
131 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites"> 132 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
132 <label>Missed Cleavages Allowed</label> 133 <label>Missed Cleavages Allowed</label>
133 <option value="0">0</option> 134 <option value="0">0</option>
134 <option value="1">1</option> 135 <option value="1">1</option>
135 <option value="2">2</option> 136 <option selected="true" value="2">2</option>
136 </param> 137 </param>
137 138
138 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/> 139 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/>
139 140
140 <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/> 141 <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>
141 142
142 <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search. Maximum is 16"/> 143 <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search. Maximum is 16"/>
143 144
144 <param name="enzyme" type="select" format="text"> 145 <param name="enzyme" type="select" format="text">
145 <label>Enzyme</label> 146 <label>Enzyme</label>
146 <option value="[R]|{P}">argc - [R]|{P}</option> 147 <option value="[R]__pc__{P}">argc - [R]|{P}</option>
147 <option value="[X]|[D]">aspn - [X]|[D]</option> 148 <option value="[X]__pc__[D]">aspn - [X]|[D]</option>
148 <option value="[FLMWY]|{P}">chymotrypsin - [FLMWY]|{P}</option> 149 <option value="[FLMWY]__pc__{P}">chymotrypsin - [FLMWY]|{P}</option>
149 <option value="[R]|[X]">clostripain - [R]|[X]</option> 150 <option value="[R]__pc__[X]">clostripain - [R]|[X]</option>
150 <option value="[M]|{P}">cnbr - [M]|{P}</option> 151 <option value="[M]__pc__{X}">cnbr - [M]|{X}</option>
151 <option value="[AGILV]|{P}">elastase - [AGILV]|{P}</option> 152 <option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option>
152 <option value="[D]|{P}">formicacid - [D]|{P}</option> 153 <option value="[D]__pc__{P}">formicacid - [D]|{P}</option>
153 <option value="[DE]|{P}">gluc - [DE]|{P}</option> 154 <option value="[DE]__pc__{P}">gluc - [DE]|{P}</option>
154 <option value="[E]|{P}">gluc_bicarb - [E]|{P}</option> 155 <option value="[E]__pc__{P}">gluc_bicarb - [E]|{P}</option>
155 <option value="[W]|[X]">iodosobenzoate - [W]|[X]</option> 156 <option value="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option>
156 <option value="[K]|{P}">lysc - [K]|{P}</option> 157 <option value="[K]__pc__{P}">lysc - [K]|{P}</option>
157 <option value="[K]|[X]">lysc-p - [K]|[X]</option> 158 <option value="[K]__pc__[X]">lysc-p - [K]|[X]</option>
158 <option value="[X]|[K]">lysn - [X]|[K]</option> 159 <option value="[X]__pc__[K]">lysn - [X]|[K]</option>
159 <option value="[X]|[AKRS]">lysn_promisc - [X]|[AKRS]</option> 160 <option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</option>
160 <option value="[X]|[X]">nonspecific - [X]|[X]</option> 161 <option value="[X]__pc__[X]">nonspecific - [X]|[X]</option>
161 <option value="[FL]|[X]">pepsina - [FL]|[X]</option> 162 <option value="[FL]__pc__[X]">pepsina - [FL]|[X]</option>
162 <option value="[P]|[X]">protein_endopeptidase - [P]|[X]</option> 163 <option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option>
163 <option value="[E]|[X]">staph_protease - [E]|[X]</option> 164 <option value="[E]__pc__[X]">staph_protease - [E]|[X]</option>
164 <option value="[FMWY]|{P},[KR]|{P},[X]|[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option> 165 <option value="[FMWY]__pc__{P},[KR]__pc__{P},[X]__pc__[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>
165 <option value="[KR]|{P}" selected="true">trypsin - [KR]|{P}</option> 166 <option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option>
166 <option value="[FKLMRWY]|{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option> 167 <option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>
167 <option value="[KR]|{P},[M]|{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option> 168 <option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>
168 <option value="[DEKR]|{P}">trypsin_gluc - [DEKR]|{P}</option> 169 <option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option>
169 </param> 170 </param>
170 171
171 172
172 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/> 173 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/>
173 174
174 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/> 175 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>
175 <param name="precursor_tolu" type="select" format="text"> 176 <param name="precursor_tolu" type="select" format="text">
176 <label>Precursor Ion Tolerance Units</label> 177 <label>Precursor Ion Tolerance Units</label>
177 <option value="ppm">ppm</option> 178 <option value="ppm">ppm</option>
178 <option value="Da">Da</option> 179 <option value="Da">Da</option>
179 </param> 180 </param>
180 181
181 <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="" falsevalue=""/> 182 <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="--multi-isotope-search" falsevalue=""/>
182 183
183 </inputs> 184 </inputs>
184 185
185 186
186 <outputs> 187 <outputs>
187 <data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/> 188 <data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/>
188 </outputs> 189 </outputs>
189 190
190 191 <tests>
192 <!-- Just test that the tool runs and produces vaguely correct output -->
193 <test>
194 <param name="source_select" value="input_ref"/>
195 <param name="fasta_file" value="testdb.fasta" format="fasta"/>
196 <param name="input_file" value="tiny.mzML" format="mzml"/>
197 <output name="output" format="tandem">
198 <assert_contents>
199 <has_text text="tandem-style" />
200 </assert_contents>
201 </output>
202 </test>
203 </tests>
191 <help> 204 <help>
192 205
193 **What it does** 206 **What it does**
194 207
195 Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores. 208 Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.